After trying for a week to identify the right frequency and combination of radiation used to destroy the Harvesters, test number 375 works. Bashir and O'Brien are ecstatic, as well as the other doctors involved in their destruction. AmbassadorSharat is pleased, and grateful for their work but as he reminds them, that is only half the task. All data pertaining to them must also be destroyed, as well as the very large stockpile on each side.

However, when they run the cycle on the final batch of cylinders, two Kellerun soldiers enter, and begin shooting. Bashir and O'Brien manage to disarm two of them, and get rid of all the soldiers, blowing out the genetic bath in the process. Unfortunately, all of the scientists were killed before they could react. When they cannot contact their runabout for a beam out, O'Brien transports them to the surface and sets the system to overload.

Meanwhile, Sharat and Ambassador E'Tyshra arrive at the station to give their condolences. They explain that everyone in that room, including many of their greatest scientists, were killed when Chief O'Brien accidentally set off a security device, and flooded the room with high-intensity radiation. Sisko doesn't believe it, but they show him the record of the internal security sensors, and ask him to extend their sincere sympathies to the families.

Down on the planet, Bashir and O'Brien find a bunker, and hide there with their assault rifles, while Bashir opens a crate of medical supplies. O'Brien still can't figure out why the Kellerun would break their treaty. Either way, the way he sees it, they have to stay put; sensors will detect them if they make it a kilometer. They also find a very old com system, which O'Brien thinks he can get working – if Bashir will shut up and let him do his job.

Back on the station, the rest of the senior staff looks at the video. It shows things as they happened when the last cylinder was destroyed. But after that, O'Brien is baffled by a strange file which suddenly appears. He can't shut it down, when he tries cutting the power, a flash of radiation vaporizes them all. Odo wants to do his own investigation, Major Kira Nerys can't believe it, and Jadzia Dax tells Starfleet they need replacements for Chief Medical Officer and Chief of Operations. Sisko also has to go tell Keiko O'Brien what happened.

While O'Brien is fixing the transmitter, Bashir teases him about his being married with all the T'Lani women who would be running around. Bashir says marriage isn't fair to them with the lives in Starfleet they lead. The Chief, however, grabs a blanket, feeling quite cold. When Bashir scans him with the medical tricorder, he finds that his blood pressure is low, and he has a fever. He was near the genetic bath when it shattered, and he has been infected with the harvesters.

When Sisko tells Keiko, he doesn't have to say much. She can read it all in his face. He agrees to give her a copy of the recording, and there isn't much else he can do.

When the Chief's eyes get fuzzy, Bashir takes directions from him. His condition slowly worsens, almost falling asleep.

On the station, Kira and Dax talk about Bashir all night, and even Quark gives him a toast. The next day, Keiko comes up and asks to see Commander Sisko. She shows him, Kira, and Dax a part of the recording where O'Brien drinking coffee. According to the time index, it is late in the afternoon, and she says he never drinks coffee in the afternoon, because it keeps him up all night. She is convinced the footage has been altered. Sisko isn't sure, but he joins Lieutenant Dax to get the Ganges a day early, just to see what's going on.

Bashir finds the problem: the contacts on the sub-processor are corroded. He cleans them with a sterile pad. It is getting harder and harder for O'Brien to stay awake. Bashir tells O'Brien about a ballet dancer he fell in love with, how they would finish each other's thoughts, and were crazy about each other. Her father even offered him a job in Paris that would lead to being chief of surgery within five years, but he didn't take it, because he couldn't have a Starfleet career. When he puts it back in the unit, they get power, but the transmitter still doesn't work. When O'Brien gets up to take a look at it, he falls right down again; he can't feel his legs.

As Sisko and Dax arrive to collect the runabout, Bashir gets the transmitter working, and sets it to a distress signal. O'Brien then gives Bashir his answer: marriage is the greatest adventure of them all. Sisko also examines the station where the accident occurred, and asks E'Tyshra about the accident, including if Sharat could have (hypothetically) modified the data clip. She doesn't see any reason why he would; the lasting peace is because both sides trust each other.

That's when Dax makes a discovery: an erased log in the Ganges computer reveals that a transport request was made 3 minutes after the fail-safe device supposedly went off, proving they were still alive at that time.

As O'Brien's condition continues to deteriorate, Bashir hears something outside. He grabs a rifle, and is surprised to find it is Ambassador E'Tyshra. When Bashir was about to explain that the T'Lani have broken the treaty, Ambassador Sharat walks through the door, and they are both on the same side. After taking his weapon, they explain to Bashir that part of their destruction of information is killing the people who know it. Otherwise, they could be recreated by them, a risk they refuse to live with.

As they are about to fire, Chief O'Brien suddenly tells them to wait, and has Bashir help him up so he can die "on his feet." As he is saying that it has been an honor serving with Bashir, they are beamed away.

Bashir explains the situation as quickly as he can to Sisko. When Sisko wants to send out a distress call, Dax says that there is a broad band inversion in place, wiping out communications and short-range sensors. Using this, Sisko plans a deception.

After refusing to release O'Brien and Bashir to the T'Lani cruiser, Sisko puts the runabout on a collision course, forcing the conspirators to destroy it. When they are about to take the other runabout in tow, they find it is gone. All they can find is a Federation warp signature. They conclude Sisko beamed aboard the runabout and piloted the first by remote.

Back on the station Bashir and O'Brien are better friends, although O'Brien has to subtly nudge Bashir into giving him some privacy. Keiko is surprised when her husband informs her that he does in fact drink coffee in the afternoon, revealing that the grounds she had for believing the recording was fake (and thereby enabling his and Bashir's rescue) were entirely baseless and they're still alive through pure luck.

"Women! That's all you ever think about."
"No it isn't... Though I do think about them a lot."

- Miles O'Brien and Julian Bashir

"To our dear departed comrades... we may have had our differences, but I'll say this for them--and it's the highest tribute I can think of: They were good customers. They always paid their bar bills on time."
"...Thats it?"
"I'm not done yet. At times like this, I'm reminded of the 57th Rule of Acquisition. Good customers are as rare as latinum... treasure them."

- Quark to Kira and Dax, about Julian Bashir and Miles O'Brien when they were presumed dead

Writer Morgan Gendel's original pitch for this episode involved a Federation team going to an alien civilization and demanding that they destroy their biogenic weaponry. However, the alien race encode the weapon into O'Brien's DNA, meaning that if the Federation want to destroy the weapon, they must kill O'Brien. (Star Trek: Deep Space Nine Companion)

Michael Piller changed Gendel's original idea to the plot now seen in the finished episode (i.e . the aliens try to kill O'Brien and Bashir; O'Brien accidentally gets infected; he and Bashir escape; the aliens set out to kill them), and Gendel composed a new teleplay with instructions from Piller to make it like a 'chase movie'. Gendel wrote his new script based upon this generic type, indeed, he even watched the films Midnight Run and North by Northwest. However, as pre-production got underway, it quickly became apparent that his script, including as it did a number of new ships, several completely new locations, and several exteriors, was financially impossible. As such, the chase aspect of the episode was removed altogether, and, as Ira Steven Behr jokes, "It became a chase movie on one set." (Star Trek: Deep Space Nine Companion)

This episode is generally seen as the beginning of the O'Brien/Bashir relationship which would become so important over the next few years (even though it is worth noting that they did have an episode together in the first season, "The Storyteller"). According to Alexander Siddig, "That was our first real 'We're stuck together. Nothing we can do about it.' And that's the crux of the relationship. It's as if these two love to hate each other, and they always seem to be stuck together, and although they voluntary walked into the bar together. But nevertheless, it's 'What am I doing stuck here with you?' 'I don't know.' I guess people have friends like that. And this is where that started off." (Crew Dossier: Julian Bashir, DS9 Season 6 DVD, Special Features)

Alexander Siddig considers "Armageddon Game" to be an important episode for Bashir and his friendship with O'Brien. Siddig commented: "That was the first time I had been allowed to take a two-hander on the show. That's not done too often because you're essentially wiping out the rest of the cast; you're not giving anyone else anything to do, and you're trusting the show to a couple of actors. I really enjoyed that and it was the first time I really got to work with Colm Meaney. We built out characters' foundational relationship on that show. We got in each other's faces and bickered and had personal things to say about each other. That was one of my most important shows". (The Official Star Trek: Deep Space Nine Magazine, issue 14, p 22)